Contacts of the helix formed by residues 470 - 487 (chain A) in PDB entry 3QHE
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 470 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A ARG* 3.5 11.4 + - - -
466A MET 3.0 2.2 + - - -
467A ASN* 3.8 8.2 + - - -
468A GLU 3.6 2.8 - - - -
469A LEU* 1.3 77.0 - - - +
471A GLY* 1.3 64.0 + - - +
472A LEU* 3.3 3.5 + - - -
473A GLN* 3.4 11.9 + - - +
474A ALA 3.2 15.6 + - - -
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Residues in contact with GLY 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU* 3.7 25.8 - - - -
466A MET* 2.8 29.3 + - - -
467A ASN* 4.9 0.6 - - - +
469A LEU 3.3 0.8 - - - -
470A GLY* 1.3 69.3 - - - +
472A LEU* 1.3 65.9 + - - +
474A ALA* 3.1 2.8 + - - +
475A ILE* 2.9 34.7 + - - +
508A LEU* 4.7 0.7 - - - -
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Residues in contact with LEU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A MET 4.8 1.4 + - - -
467A ASN* 5.2 3.4 + - - +
470A GLY 3.3 0.6 - - - -
471A GLY* 1.3 76.0 - - - +
473A GLN* 1.3 69.2 + - - +
475A ILE 3.3 0.2 + - - -
476A ALA* 2.9 25.6 + - + +
505A LEU* 3.6 23.6 - - + +
508A LEU* 4.0 32.3 - - + +
509A THR* 4.3 14.8 - - + -
515A ASN* 4.0 36.8 - - + +
518A THR* 4.0 23.1 - - + -
519A LEU* 4.0 28.0 - - + +
522A MET* 4.7 0.4 - - - -
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Residues in contact with GLN 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ARG* 6.3 0.2 - - - +
470A GLY* 3.4 12.6 + - - +
471A GLY 3.3 0.6 - - - -
472A LEU* 1.3 84.5 - - - +
474A ALA* 1.3 58.5 + - - +
476A ALA* 3.6 1.7 - - - +
477A GLU* 2.9 56.7 + - - +
518A THR* 4.9 12.0 - - + +
522A MET* 3.7 20.5 - - + +
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Residues in contact with ALA 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU* 4.4 7.6 - - + -
413A ILE* 3.5 22.8 - - + +
414A ARG* 4.2 31.9 - - + +
417A CYS* 4.6 2.4 - - - -
470A GLY 3.2 10.5 + - - +
471A GLY 3.1 9.4 + - - +
473A GLN* 1.3 80.2 - - - +
475A ILE* 1.3 62.5 + - - +
477A GLU* 3.4 13.6 + - - +
478A LEU* 3.2 18.2 + - - +
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Residues in contact with ILE 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A LEU* 4.7 1.1 - - + -
413A ILE* 3.8 8.5 - - + -
450A VAL* 5.1 5.4 - - + -
453A LEU* 3.8 36.8 - - + -
466A MET* 4.8 5.6 - - - -
471A GLY* 2.9 26.6 + - - +
472A LEU 3.9 2.7 - - - +
474A ALA* 1.3 69.0 - - - +
476A ALA* 1.3 65.6 + - - +
478A LEU* 3.5 4.9 + - + +
479A LEU* 3.2 20.6 + - - +
501A ALA* 3.6 39.7 - - + +
504A ALA* 4.2 12.3 - - + -
505A LEU* 4.1 8.1 - - + -
508A LEU* 3.9 25.1 - - + -
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Residues in contact with ALA 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LEU* 2.9 18.4 + - + +
473A GLN 3.6 4.3 - - - +
475A ILE* 1.3 77.4 - - - +
477A GLU* 1.3 56.1 + - - +
479A LEU* 3.2 4.6 + - - +
480A GLN* 2.9 29.3 + - - +
505A LEU* 4.0 13.4 - - + +
519A LEU* 3.7 26.9 - - + -
522A MET* 3.6 18.6 - - + -
525A CYS* 3.5 9.5 - - - -
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Residues in contact with GLU 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A ARG* 5.5 6.1 + - - +
417A CYS* 3.9 7.0 - - - +
421A TRP* 3.8 37.7 + - + -
473A GLN* 2.9 49.6 + - - +
474A ALA* 3.6 12.2 - - - +
476A ALA* 1.3 76.5 - - - +
478A LEU* 1.3 56.3 + - - +
480A GLN* 3.3 12.6 + - - +
481A VAL* 2.9 32.2 + - - +
522A MET* 3.7 15.1 - - + +
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Residues in contact with LEU 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413A ILE* 4.1 22.7 - - + -
416A TYR* 3.6 36.3 - - + -
417A CYS* 3.6 15.8 - - - -
446A ILE* 3.9 9.4 - - + -
450A VAL* 3.4 38.8 - - + -
474A ALA 3.2 10.0 + - - +
475A ILE* 3.6 10.5 - - - +
476A ALA 3.3 0.2 - - - -
477A GLU* 1.3 75.7 - - - +
479A LEU* 1.3 65.2 + - - +
481A VAL* 3.3 3.6 + - + +
482A ASP* 3.0 24.6 + - + +
497A LEU* 4.1 17.3 - - + -
501A ALA* 5.0 2.7 - - + -
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Residues in contact with LEU 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475A ILE 3.2 11.0 + - - +
476A ALA* 3.5 8.5 - - - +
478A LEU* 1.3 79.9 - - - +
480A GLN* 1.3 69.3 + - - +
482A ASP* 3.9 3.9 - - - +
483A CYS* 3.0 46.1 + - - -
497A LEU* 5.1 4.3 - - - -
498A ARG* 4.3 15.3 - - + +
501A ALA* 4.2 9.9 - - + -
502A GLY* 4.3 19.1 - - - +
505A LEU* 4.1 15.7 - - + -
525A CYS* 4.4 5.6 - - - -
528A ALA* 4.3 8.7 - - + -
529A LEU* 3.7 34.3 - - + +
532A GLN* 5.1 2.0 - - + -
544A ILE* 4.5 6.7 - - + -
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Residues in contact with GLN 480 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A TRP* 6.0 3.9 - - - +
476A ALA 2.9 13.1 + - - +
477A GLU* 3.5 16.9 - - - +
478A LEU 3.2 0.2 - - - -
479A LEU* 1.3 84.5 - - - +
481A VAL* 1.3 59.1 + - + +
483A CYS* 3.2 2.9 + - - +
484A GLU* 2.9 57.2 + - + +
522A MET* 4.8 6.6 - - - +
524A GLY* 3.6 18.1 + - - +
525A CYS* 3.3 33.6 + - - +
528A ALA* 4.1 6.5 - - + +
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Residues in contact with VAL 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 4.8 1.3 - - + -
417A CYS* 4.2 10.3 - - - -
420A CYS* 3.7 34.5 - - + -
421A TRP* 3.6 34.5 - - + +
424A GLN* 3.8 16.8 - - - +
477A GLU 2.9 18.4 + - - +
478A LEU* 3.5 19.7 - - + +
480A GLN* 1.3 74.1 - - + +
482A ASP* 1.3 61.5 + - - +
484A GLU* 3.3 6.5 + - - +
485A MET* 2.9 35.8 + - - +
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Residues in contact with ASP 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 4.7 4.1 + - + +
441A PRO* 4.2 9.5 - - - +
478A LEU* 3.0 19.0 + - + +
479A LEU 3.9 2.5 - - - +
481A VAL* 1.3 79.3 - - + +
483A CYS* 1.3 61.2 + - - +
485A MET* 4.5 7.0 - - - -
486A TYR* 3.0 29.4 + - - -
494A SER* 3.0 27.0 + - - -
497A LEU* 4.2 25.4 - - + +
498A ARG* 2.8 48.9 + - + +
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Residues in contact with CYS 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479A LEU* 3.0 41.4 + - - -
480A GLN 3.4 7.4 - - - +
482A ASP* 1.3 77.2 - - - +
484A GLU* 1.3 58.6 + - - +
487A GLY* 2.9 30.0 + - - -
498A ARG* 3.6 21.5 - - - +
528A ALA* 3.8 13.9 - - + -
532A GLN* 3.4 39.3 + - - +
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Residues in contact with GLU 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421A TRP* 5.8 0.3 + - - -
424A GLN* 2.9 32.4 + - - +
480A GLN* 2.9 51.1 + - + +
481A VAL* 3.8 5.9 - - - +
483A CYS* 1.3 78.4 - - + +
485A MET* 1.3 63.6 + - - +
487A GLY* 4.3 2.3 + - - -
524A GLY* 4.4 6.1 - - - +
527A ARG* 5.7 1.0 + - - -
528A ALA* 5.5 3.6 - - + -
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Residues in contact with MET 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416A TYR* 4.1 5.8 - - - +
420A CYS* 3.5 39.7 - - + -
423A TRP* 4.2 21.3 - - + -
424A GLN* 4.9 3.8 - - + +
438A MET* 3.5 44.8 - - + +
439A PRO* 3.8 13.2 - - + +
481A VAL* 2.9 29.4 + - + +
482A ASP* 4.5 2.2 - - - -
484A GLU* 1.3 78.5 - - - +
486A TYR* 1.3 87.8 + - + +
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Residues in contact with TYR 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A TYR* 4.9 0.2 - - - -
438A MET* 3.8 20.1 - - + +
439A PRO 3.2 24.1 + - - -
440A ALA* 4.0 2.6 - - - +
441A PRO* 3.4 22.1 - - + +
482A ASP* 3.0 35.0 + - - -
485A MET* 1.3 98.0 - - + +
487A GLY* 1.3 64.8 + - - +
488A LEU 3.6 0.5 + - - -
489A THR* 3.7 24.4 + - + -
494A SER* 3.8 8.7 - - - -
498A ARG* 3.6 12.6 - - - +
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Residues in contact with GLY 487 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A CYS 2.9 19.4 + - - -
484A GLU 4.3 1.9 + - - -
485A MET 3.7 1.2 - - - -
486A TYR* 1.3 77.3 - - - +
488A LEU* 1.3 56.5 + - - -
489A THR 2.8 13.7 + - - -
498A ARG* 2.9 25.7 + - - -
532A GLN* 5.4 1.8 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il